This section introduces aspects that may help facilitate a better understanding of the disclosure. Accordingly, these statements are to be read in this light and are not to be understood as admissions about what is or is not prior art.
DNA relaxation catalyzed by topoisomerase IB (Top1) is essential for replication and transcription in vertebrate cells. During this enzyme-mediated process, covalent Top1-DNA cleavage complexes are produced. Normally, cleavage complexes reverse rapidly and are undetectable in cells. However, DNA damage and certain cancer chemotherapeutic agents known as Top1 poisons can stabilize the cleavage complexes by preventing their reversal. As a result of the extended lifetimes of the cleavage complexes, advancing replication forks can collide with the DNA cleavage sites and produce DNA double-strand breaks. The DNA damage eventually causes the cell to enter apoptosis (Pommier, Y. DNA Topoisomerase I Inhibitors: Chemistry, Biology, and Interfacial Inhibition. Chem. Rev. 2009, 109, 2894-2902).
Several distinct Top poison chemotypes have been developed since the discovery of the natural product camptothecin (1, Scheme 1) and its unique mechanism of action (Oberlies, N. H., et al., J. Nat. Prod. 2004, 67, 129-135). Two derivatives of camptothecin are FDA-approved drugs used for the treatment of solid tumors, and several analogues are being investigated for the treatment of various cancers (Pommier, Y., et al., Chem. Biol. 2010, 17, 421-433). The potent anticancer activities of the members of this class are counterbalanced by problems with physicochemical properties, drug resistance, and patient tolerability. The shortcomings of the camptothecins include: (1) poor water solubility; (2) instability of the E-ring lactone at physiological pH, which hydrolyzes to a hydroxyacid that binds to plasma proteins; (3) rapid diffusion from their binding site in the Top1-DNA cleavage complexes, which may necessitate longer drug infusion times in order to maintain adequate concentrations of the ternary cleavage complexes; (4) dose-limiting toxicities including bone marrow suppression and severe dose-limiting diarrhea; (5) susceptibility to drug resistance by several Top1 point mutations; and (6) efficient removal from cancer cells by drug efflux pumps that results in drug resistance. There are still unmet clinical needs for better treatment options.
These limitations have resulted in the discovery of improved Top1 poisons. Two compounds, the indenoisoquinolines indotecan (LMP400, 2) and indimitecan (LMP776, 3), have been promoted to Phase I clinical trials at the National Cancer Institute (S. Kummar, et al., Cancer Chemother Pharmacol (2016) 78:73-81).
A third, structurally related indenoisoquinoline known as MJ-III-65 (LMP744, 4) has shown promising preclinical activity (Antony, S. et al., Mol. Pharmacol. 2005, 67, 523-530). The indenoisoquinolines overcome many of the drawbacks associated with the camptothecins (Pommier, Y. Nat. Rev. Cancer 2006, 6, 789-802).
Tyrosyl DNA phosphodiesterases 1 and 2 (TDP1 and TDP2) are DNA repair enzymes that process Top1- and Top2-mediated DNA lesions, respectively. TDP1 catalyzes the hydrolysis of the 3′-phosphotyrosyl-DNA linkages that result from degradation of Top1-DNA cleavage complexes. Bis(indenoisoquinoline) 5 displays potent Top1 inhibitory activity and its IC50 values versus purified and whole cell extract-containing TDP1 are each approximately 1 μM. TDP2 catalyzes the hydrolysis of the 5′-phosphotyrosyl-DNA linkages that result from degradation of Top2-DNA cleavage complexes and it also displays weak activity against 3′-phosphotyrosyl-DNA linkages. There are currently no promising TDP2 inhibitor series. A series of deazaflavins (e.g. 6) with low nanomolar TDP2 inhibitory potencies was recently reported. However, the authors remarked that the chemical series is marred by poor cellular permeability. TDP1 and TDP2 can serve as mutual backups for the repair of stalled Top1-DNA cleavage complexes, which would make dual TDP1 and TDP2 inhibition a significant advancement.
